I'm a bit confused, Tim. Did you get your own ISBN through Amazon? If that's the case, they technically own the ISBN and you can't use it anywhere else. Your recourse is to take it down and republish it with your own ISBN. I'm getting a nervous sense of legalize though when I tell you this and that makes my advice a bit wary. Researching ISBNs can give you a really big headache--or boredom. For instance, there are legal differences in ISBN in other countries. In the US, you have to buy them if you use them. Not so in Canada and, I'd think, in your home in Australia.
Could you use a different ISBN? Why not? The problem is some book stores will search your books by ISBN and if they come across the one with less sales, or an old summary, or some confusion on book ID, whatever ... it could be an issue. It's a fairly small issue though, I'd think. You use a separate ISBN for ebooks anyway. D2D might provide an optional ISBN for paperbacks, but I'm not sure. I know they offer this for ebooks.
Let me tell you what I do, if it'd help: I use Ingram for paperbacks wide. I have ONE ISBN for Ingram and Amazon. I bought the ISBNs through Bowker. I have my own distinct ISBN under my own publisher not affiliated with Amazon.
Should you use D2D? Are you committed? I use D2D for Apple ebook distribution. I haven't fully researched them for paperbacks. As far as wide distribution and Ingram, I've admittedly had problems with Ingram but they have their fingers in the most stores worldwide. They have a monopoly on paperbacks, essentially. They are the Amazon of paperbacks. My blood pressure has suffered using Ingram but then it's suffered through Amazon too.
The main thorn for me with publishing paperbacks wide paperbacks is formatting a different cover. Other than that, I use the same pdf file in both Ingram and Amazon. Hopefully all this helps.